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Very Odd UnZipping Issue

I'm having an issue in php. I have a zip file that is uploaded to the server. I need to unzip the file and then play with it's contents.

If I manually ssh onto the server via www-data (the same user account as apache runs in), I can type

# unzip -u base.zip -d /full/dest/path

And all of the zip files contents are decompressed. BUT if I have my php code run

exec('unzip -u base.zip -d /full/dest/path');

some of the files from the zip file are unzipped but others are outright missing from the destination directory. The code continues to process after the exec() statement and there are no errors in the apache log files.